Storage is the critical operation within the biomass supply chain to reduce feedstock supply risks and to manage smooth year-around operations of a biorefinery or a bioenergy plant. This paper analyzed the economic and environmental impacts of four different biomass storage systems for woodchips (Outdoor-open, Outdoor-tarped, Indoor, and Silo) and two systems for pellets (Indoor and Silo). Storage cost includes the costs for handling (including ventilation in case of silo storage), infrastructure investment, and dry matter loss (DML) for each system. The estimation of total greenhouse gas (GHG) emissions includes the fugitive emissions from storage piles and emissions due to electricity and fuel consumption for each system. Among four storage systems, the outdoor-tarped ($15.0 ODMT−1, ODMT: Oven Dry Metric Ton) and silo ($5.8 ODMT−1) storage were the least-cost options for woodchips and pellets respectively. However, silo-storage could be the most promising option for storing woodchips ($5.8 ODMT−1) and pellets ($2.3 ODMT−1), if it is used for short-term (two months) and frequently (at least six times) in a year. The total GHG emissions for six-month storage were 2.8–11.8 kgCO2e ODMT−1 for woodchips and 8.6–42.0 kgCO2e ODMT−1 for pellets. During Outdoor-open storage, the lower heating value of woodchips could drop to 37% due to increased dry-matter loss (DML) and moisture content. The initial moisture content, bulk density, DML, and resource required during handling were the most sensitive parameters influenced the storage performances of both woodchips and pellets. This study has demonstrated that a combination of different storage options along the supply chain could reduce the total biomass storage cost for a biorefinery or power plant.